Kongtrul Yonten Gyatso was born in the hidden valley of Rongyap (rong rgyab), which lies in front of Mount Pema Lhartse (padma lha rtse) in Drida Zalmogang (‘bri zla zal mo sgang) in East Tibet, on the tenth day of the tenth month in the Water Bird year of the fourteenth calendrical cycle. (December 2, 1813). His actual father, Lama Yundrung Tendzin (g.yung drung bstan ‘dzin), was successor of the Khyungpo (khyung po) clan; and his mother was Tashi Tso (bkra shis mtsho). His stepfather was a lay Bön practitioner Sonam Pel (bsod nams 'phel).
From a young age Jamgon Kongtrul showed outstanding mental abilities. In his youth, due to help of Karma Phuntsok (karma phun tshogs) he studied the medical treatise "Four Tantras" (rgyud bzhi) and got acquainted with herbs. Then, on the recommendation of Karma Ngedon (karma nges don) he studied countless sutras, tantras and commentaries with around fifty great masters of all traditions: including outstanding scientist Gyurme Thutob Namgyal (‘gyur med mthu stobs rnam rgyal, b. 1787) from Shechen (zhe chen) monastery, Situ Pema Nyinje Wangpo (si tu padma nyin byed dbang po, 1774–1853) from Palpung (dpal spung) monastery, Jamyang Khyentse Wangpo (‘jam dbyangs mkhyen brtse’i dbang po, 1820–1892) and many others. At Karma Tsewang Rabten (karma tshe dbang rab brtan) he learned the art of medical procedures.
Kongtrul Yonten Gyatso was a respected authority in all five traditional sciences of Tibet, and the author of about ninety volumes on different topics. His compilation "Five Great Treasures" (mdzod chen lnga), named by Jamyang Khyentse Wangpo, is traditionally considered to be his principal work.

1. The Treasury of Encyclopedic Knowledge - extensive teachings on the basis, path and fruit, completely covering the entire corpus of sutras and tantras, fields of conventional sciences and up to the highest of the nine unconventional chariots-Dzogchen Ati Yoga.
2. The Treasury of Precious Termas (rin chen gter mdzod) - 60 volumes containing numerous large and small termas, opened by great tertons Sangye Lama Lingpa (sangs rgyas bla ma gling pa, XI c.), Pema Osal Dongak Lingpa (padma ‘od gsal mdo sngags gling pa — the terton name of Jamyang Khyentse Wangpo), Chogyur Dechen Lingpa (mchog gyur bde chen gling pa, 1829–1870) and many others.
3. The Treasury of Precious Instructions (gdams ngag mdzod) - 12 volumes containing mandalas, empowerments and instructions for each tantra separately belonging to the eight great chariots of the practice lineage.
4. The Treasury of Kagyu Mantras (bkа' brgyud sngags mdzod) - 6 volumes containing thirteen tantric practice of deities, as well as ancient and modern tantras (some of them were given by Marpa the translator), followed by the tantric teachings of the completion stage, initiation rituals and various text transmission.
5. The Uncommon Treasury (thun mong min gsang mdzod) – 7 volumes containing the unique secret treasures of his own profound terma revelations.

Besides all of this, he composed a large number of different works: collected praises, essays, works on medicine and other texts.
In the medical field his main works are:
"Drops of nectar - Selected notes on the essentials for young physicians" (‘tsho byed las dang po ba la nye bar mkho ba’i zin tig gces par btus pa bdud rtsi’i thigs pa). This text, also known as "Kongtrul’s Notes" (kong sprul zin tig), quickly became popular all over Tibet and still is widely applied in practice by physicians.
"Quintessence of instruction by medical shining lights on the practical aspects of making and using of dngul chu btso bkru chen mo» (dngul chu btso bkru chen mo’i lag len ‘tsho byed mkhas pa’i snying bcud).
Throughout of whole his life Kongtrul Yonten Gyatso gave initiations, instructions and text transmission sutras, tantras, oral teachings of old and new termas.
Kongtrul Yonten Gyatso was one of the major figures of the nonsectarian Rimé movement, and therefore had close disciples from all Tibetan traditions: Jamyang Loter Wangpo (‘jam dbyang blo gter dbang po, 1847–1914), Choje Kunga Jamyang (chos rje kun dga’ ‘jam dbyang) and others from the Sakya school; Mipham Jamyang Namgyal (mi pham ‘jam dbyang rnam rgyal, 1846–1912), Terton Lerab Lingpa (gter ston las rab gling pa) and many others from the the Nyingma school; Karmapa XIV (Thegchog Dorje, theg mchog rdo rje, 1798–1868) и XV (Khakyab Dorje, mkha' khyab rdo rje, 1871–1922), Tai Situpa X (Pema Kunzang Chogyal, padma kun bzang chos rgyal, 1854—1885) and XI (Pema Wangchuk Gyalpo, padma dbang phyug rgyal po, 1886—1952) were followers from the the Kagyu school; Yeshe Gongpel (ye shes gong 'phal) the khenpo from Gyume Monastery (rgyud smad), Dragyab Dongtrul Khechog Ngawang Damcho Gyatso (brag yab gdong sprul ngag dbang dam chos rgya mtsho) and others were followers from the the Gelug school.
In other words, at that time many students flocked to Kongtrul Yonten Gyatso from all over Tibet- from U and Tsang region up to Amdo and Kham. Most of his students, regardless of their belonging to a particular tradition, considered this master a truly outstanding person. He was a prominent physician and did much for the development of Tibetan medicine, including collecting, preserving and disseminating medical teaching. Kongtrul Yonten Gyatso was one of the greatest masters venerated by all Buddhist tradition of Tibet.
Kongtrul Yonten Gyatso died at the eighty-seventh year of life on December 28, 1899.